is designed for displaying sheet music PDF files, but its annotation features are quite extensive and I think it might be useful to you. Of course it will work with any PDF file, not just sheet music files.

I can't compare it to any other PDF reader for the iPad, but I've been very happy with GoodReader. From the marketing spiel on iTunes:

Annotation is a feature long sought after by users who want to add their own mark-ups to PDFs, especially those collaborating as a team on shared documents. The types of annotations that can be created and edited in GoodReader include typewriter text boxes, popup comments ("sticky notes"), text highlights, freehand drawings, lines, arrows, rectangles, ovals, cloudy shapes, text underlines, strikeouts, text insertion marks.

If you want the ability to annotate PDF as well as fill out PDF forms, the best iPad app out there is PDF Expert.

PDF Expert lets you read and annotate PDF documents, highlight text,
make notes, draw with your finger and save these changes which are
compatible with Preview and Adobe Acrobat! Moreover, PDF Expert is the
only iPad application that can fill in PDF forms!

If you want additional opinions specifically dealing with annotating PDF files on an iPad, this macrumours thread has a lot of info.

I use ezPDF on Android and I see that it exists on iPhone and iPad too, for $2 and $3 respectively. It has proper PDF annotation support. While I've not used the iVersions, I'd expect they are just as awesome as the Android version.

Actually, the latest version of ibooks does offer two ways to export notes:

Via e-mail.

Via PDF provided you print to an app like printopia (Mac) or a virtual printing solution (PC).

If you need the PC solution, please respond and I will research it for you.

Also, Nook in conjunction with Nookstudy (Mac/PC) may have this feature.

The people on the web are recommending iAnnotatePDF, which can export annotations as text. They say the interface is not that great.

Possible untested Nook instructions are below:

To use the Nookstudy options:
1. Download Nookstudy. Import the PDF.
2. Ensure it shows up and can be read on Nook for ipad.
3. Annotate.
4. Go back to Nookstudy. Your changes will be there. Then, export the notes to a .doc file. (supported.)
URL: www.nookstudy.com

I would also take a serious look at Readdle's products and Goodreader.